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biomaj

biomaj(1)							   USER COMMANDS							 biomaj(1)

NAME

       biomaj - downloads and transform remote biological data banks

SYNOPSIS

       biomaj [-h]

DESCRIPTION

       BioMAJ (BIOlogie Mise A Jour) is a workflow engine dedicated
	to data synchronization and processing.The Software automates
	the update cycle and the supervision of the locally mirrored
	databank repository.  User must have roots rights to run biomaj.

OPTIONS

       -h     display the list of commands.

INSTALL

       At  installation, BioMAJ requires a database to run (MySQL), installer should first create a database (biomaj_log) and a database user (the
       one used at installation setup).
	The database configuration for biomaj can be set or modified in /etc/biomaj/db_properties/global.properties.

       In the install fails due to a SQL error, the install script must be manually run to create/upgrade the database:

       perl /usr/share/biomaj/sql/migration/update.pl

       The script will create/upgrade the database and update the configuration files.

ADMIN USER

       A default admin user (admin) is created by the scripts.	If using the biomaj-watcher, the default password (admin) MUST be changed  immedi-
       atly via the watcher interface.

       If only biomaj core is used, password is useless.
	.PP

UPGRADE

	In the case of a package upgrade, if properly configured, the migration scripts will be ran automatically at install.
	It is possible to run manually the script:
	.B See perl /usr/share/biomaj/sql/migration/update.pl -h
	for usage.

DATA BANKS

       By default, biomaj is configured (data.dir in global.properties) to write banks to /var/lib/biomaj.

EXAMPLES

       Update a bank:
	      biomaj --update genbank

       Show console
	      biomaj --update genbank --console

       Show status:
	      biomaj --status

EXIT STATUS

       biomaj returns a zero exist status if it succeeds, it does not represent the bank update status.

AUTHOR

       Olivier Sallou (olivier.sallou (at) irisa.fr) Romaric Sabas (romaric.sabas (at) irisa.fr)

version 1.2.0							September 14, 2011							 biomaj(1)